Molecular LLM Agents: From Architectural Design to Scientific Autonomy

Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM agents must perceive, reason about, and act upon chemical objects across symbolic strings, molecular graphs, 3D conformations, spectra, simulations, and wet-lab measurements. Their capabilities depend on chemically faithful molecular perception, an LLM-centered agent framework, domain-specific tool grounding, and computational or experimental feedback, in addition to planning and tool use. This work develops a conceptual framework for molecular LLM agents from two complementary perspectives. First, we introduce an architectural view of molecular-agent design, covering molecular representation and perception, the agent framework, domain-specific toolboxes, and learning and optimization. Second, we propose a scientific autonomy ladder inspired by staged autonomy in engineering systems, categorizing agents into four levels: L1 assistive or fixed workflows, L2 adaptive computational agents, L3 feedback-aware physical experiment agents, and L4 scientific-agenda agents. Together, these two perspectives establish a comprehensive framework for comparing existing molecular LLM agents, identifying missing capabilities and deployment risks, and guiding the design, evaluation, and deployment of future agents in molecular discovery workflows.

From Visual Widgets to UI Code: Efficient Tool-Grounded Generation

Existing screenshot-to-code systems face a trade-off between flexibility and controllability. Direct multimodal generation can hallucinate visible details, whereas structured pipelines reduce such errors through component-wise decomposition, predefined templates, and customized intermediate representations. These structures, however, introduce additional generative orchestration and restrict outputs to designs covered by the representation. We investigate whether selective tool grounding can improve the fidelity--efficiency trade-off of direct widget-to-code generation. We introduce \textbf{WidgetGen}, a lightweight tool-grounded framework that extracts observable text and color evidence, performs high-level layout and optional chart reasoning, and directly generates executable JavaScript XML (\emph{JSX}). This design reduces reliance on component-wise generation while avoiding a fixed UI schema. Across six multimodal models and \(1{,}000\) held-out widgets, WidgetGen outperforms direct prompting and the structured Widget2Code pipeline on most visual reconstruction metrics, with consistent gains in area, legibility, and style. Finally, reconstruction-derived image-code pairs improve six Qwen-family open-weight models across every reported metric through supervised fine-tuning. These results establish WidgetGen as a strong lightweight baseline and show that selective evidence grounding offers an effective alternative to extensive representation constraints.